Specificity and Timing the Entrance of Synthetases

The scenario displayed by our staging model indicates a faster encoding by class II duplications, which predominate strongly in the homogeneous sector. Class I enzymes predominate in the mixed sector but their numbers only equilibrate with the class II numbers in the last stage. The wide-range asynchrony of the two aRS classes has a counterpoint in the short-range concerted duplications inside each of the classes, indicating the occurrence of coupled historical inductions possibly related to the entrance of the tRNAs in pairs.

The specificity and spread of the synthetase classes is indicated to run strictly through the pairs of columns. Class II occupies fully the central G and central C columns, including the proposed early occupier of the CG box (Ala) and the first occupiers of the CA and CU boxes (presently receded to the 5' G triplets), respectively Cys and Ser, the first through the dual-specificity ProCysRS. Class I occupies fully the central A and central U columns. The homogeneity in the central A column includes the atypical PheRS, refering to its 2' mode of acylation. In the complex central U boxes, class I corresponds to the second occupiers, in the 5' Y triplets.

The spread due to class II central Y ambiguity was to the first occupiers of the central U column: UG (His), UC (Asp), and UU (Asn), plus the atypical pair UU (Lys)/AA (Phe). The dispersion of class I replaced various early class II attributions, such as the dicodonic expansions of Arg and Leu, and the homogeneous sector ended up with a greater mixture of characters than the mixed sector. Nonetheless, the homogeneous sector maintained a neat regularity in the attribution of enzymes of the same class to all tRNA pairs: the hydropathy outliers occupy two pairs with class II; the other two have either the couple of class I (EL) or the couple of atypical acylation systems (KF). We take these regularities, clearer in the homogenous than in the mixed sector, to indicate that characters of the paired tRNAs may have guided the fishing of aRS of the same class. Such regularity was partially eroded in the mixed sector. Couples of aRS class I can be seen only in the UG (Gln)/AC (Val) and in the AU (Ile, Met)/UA (Tyr) pairs, while the CA (Cys, Trp)/GU (Thr) and the CG (Arg)/GC (Ala) pairs became class-discordant after the class I displacement of the previous class II occupiers of the CA (ProCysRS) and of the CG (AlaRS) boxes. The latter two substitutions were the main symmetry-breaking events to the configuration of the code.

The mechanism of formation of the code by the fishing of complementary anti-codons is entirely consistent with the aRS class specificity for the complementary central bases, only adding a further specificity, namely that the complementary triplets are of the perfect palindromic kind, united diagonally in the matrix. This regularity is not immediately apparent from the plain observation of the overall distribution of synthetases in the matrix. Only two diagonally paired boxes are unambiguous, with synthetases of the same class: class II in the NGG/NCC pair (stage I), class I in the NAU/NUA pair (stage 4).

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